spacetx / spacetx-writer Goto Github PK

After resaving the file we tried to run StarFish on it but it keeps failing even when playing with the version numbers ... see the image.sc post here:

https://forum.image.sc/t/unrecognized-version-number-for-spacetx-files-created-with-java/57570

Thanks so much for any help!

Discussed during the 2019 SpaceJam in Seattle. Longer-term, the model may be adapted to add metadata to a channel in the main tensor.

Hi, today I tried to resave a large 3d image with 1550 z planes. I tried encoding it as "z_<0000-1549>.tif" in the filename, but that does not work. I looked at the source code and it seems that this feature is not implemented because it immediately checks that the filename exists, which of course it doesn't - it would need to be parsed first and "z_<0000-1549>.tif" would have to be expanded into 1550 filenames:

I added my 1500 filenames by hand using a for-loop instead, which works fine. So my guess would be that somehow, parsing of the filename would have to happen just before the code snippet I posted above. Or am I doing something wrong or missing something?

Thanks so much,
Stephan

I have been trying to get my .nd2 images in spacetx format, but since I have many FOVs ~2TB in size across 12 rounds on an individual FOV basis (i.e. sect1_Time00000_Point0007_ChannelL-750,DAPI,L-488_Seq0007.nd2), I really struggled to load them with the existing starfish tutorials without having to split them tediously into separate DAPI and FISH channels.

I was hoping the spacetxx-writer would help, and from the looks of it, it built without issues using docker. I did not get an error message. The last few lines of the build were:

=> exporting to image                                                                                                                0.1s 
=> => exporting layers                                                                                                               0.1s 
=> => writing image sha256:a735297a4368641df2b309ffeab42a1116d60022dabef2059c9fbc0010b9ac92                                          0.0s 
=> => naming to docker.io/library/spacetx-writer  

When trying to run spacetx-writer, I get the following error:
zsh: command not found: spacetx-writer

I am not certain if something went wrong with the build, or what I am doing wrong. I followed the usage instructions of the simple example with my filenames, but find it a little hard to trouble shoot.

I am running this on a Mac OsX Ventura 13.3.1 (M1 Max, 32GB)

Is there interest in trying to get this building again? Or would archiving the repo be more appropriate?

Spacetx-writer does not convert a custom codebook.csv into codebook.json.
I was wondering if I have to write my codebook in a specific way or format that makes it usable for the conversion.

It would be useful if image/plane greater then Starfish 3Kx3K threashold (spacetx/starfish#627) could be retiled to 2D files for processing large fields of views

Simillar to what is possible in bfconvert https://docs.openmicroscopy.org/bio-formats/6.2.1/users/comlinetools/conversion.html#cmdoption-bfconvert-tilex

No more than approx. 10^3 files should be placed in the same directory. If necessary, artificial prefix directories should be generated (e.g. 000/first-batch-of.tiff)